go home Home | Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Data Structures | File List | Namespace Members | Data Fields | Globals | Related Pages
Public Types | Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes
itk::AffineDTI3DTransform< TScalarType > Class Template Reference

#include <itkAffineDTI3DTransform.h>

Detailed Description

template<class TScalarType = double>
class itk::AffineDTI3DTransform< TScalarType >

AffineDTI3DTransform of a vector space (e.g. space coordinates)

This transform applies an affine transformation, but is parameterized by angles, shear factors, scales, and translation, instead of by the affine matrix. It is meant for registration of MR diffusion weighted images, but could be used for other images as well of course.

The affine model is adopted from the following paper: [1] A. Leemans and D.K. Jones. "The B-matrix must be rotated when correcting for subject motion in DTI data". Magnetic Resonance in Medicine, Volume 61, Issue 6, pages 1336 - 1349, 2009.

The model is as follows:
T(x) = R G S (x-c) + t + c
with:

Using this model, the rotation components can be easily extracted an applied to the B-matrix.

The parameters are ordered as follows: in 2D: [ Angle ShearX ShearY ScaleX ScaleY TranslationX TranslationY ] in 3D: [ AngleX AngleY AngleZ ShearX ShearY ShearZ ScaleX ScaleY ScaleZ TranslationX TranslationY TranslationZ ]

The serialization of the fixed parameters is an array of 2 elements defining the center of rotation.

This transform applies an affine transformation, but is parameterized by angles, shear factors, scales, and translation, instead of by the affine matrix. It is meant for registration of MR diffusion weighted images, but could be used for other images as well of course.

The affine model is adopted from the following paper: [1] A. Leemans and D.K. Jones. "The B-matrix must be rotated when correcting for subject motion in DTI data". Magnetic Resonance in Medicine, Volume 61, Issue 6, pages 1336 - 1349, 2009.

The model is as follows:
T(x) = R G S (x-c) + t + c
with:

Using this model, the rotation components can be easily extracted an applied to the B-matrix.

The parameters are ordered as follows: [ AngleX AngleY AngleZ ShearX ShearY ShearZ ScaleX ScaleY ScaleZ TranslationX TranslationY TranslationZ ]

The serialization of the fixed parameters is an array of 3 elements defining the center of rotation.

Definition at line 78 of file itkAffineDTI3DTransform.h.

Inheritance diagram for itk::AffineDTI3DTransform< TScalarType >:
Inheritance graph
[legend]

Public Types

using AngleType = typename Superclass::ScalarType
 
using CenterType = InputPointType
 
using ConstPointer = SmartPointer< const Self >
 
using InverseMatrixType = Matrix< TScalarType, Self::InputSpaceDimension, Self::OutputSpaceDimension >
 
using MatrixType = Matrix< TScalarType, Self::OutputSpaceDimension, Self::InputSpaceDimension >
 
using OffsetType = OutputVectorType
 
using Pointer = SmartPointer< Self >
 
using ScalarArrayType = FixedArray< ScalarType >
 
using Self = AffineDTI3DTransform
 
using Superclass = AdvancedMatrixOffsetTransformBase< TScalarType, 3, 3 >
 
using TranslationType = OutputVectorType
 
- Public Types inherited from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >
using CenterType = InputPointType
 
using ConstPointer = SmartPointer< const Self >
 
using InverseMatrixType = Matrix< TScalarType, Self::InputSpaceDimension, Self::OutputSpaceDimension >
 
using MatrixType = Matrix< TScalarType, Self::OutputSpaceDimension, Self::InputSpaceDimension >
 
using OffsetType = OutputVectorType
 
using Pointer = SmartPointer< Self >
 
using Self = AdvancedMatrixOffsetTransformBase
 
using Superclass = AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
 
using TranslationType = OutputVectorType
 
- Public Types inherited from itk::AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
using ConstPointer = SmartPointer< const Self >
 
using InternalMatrixType = typename SpatialJacobianType::InternalMatrixType
 
using InverseTransformBaseType = typename Superclass::InverseTransformBaseType
 
using JacobianOfSpatialHessianType = std::vector< SpatialHessianType >
 
using JacobianOfSpatialJacobianType = std::vector< SpatialJacobianType >
 
using MovingImageGradientType = OutputCovariantVectorType
 
using MovingImageGradientValueType = typename MovingImageGradientType::ValueType
 
using NonZeroJacobianIndicesType = std::vector< unsigned long >
 
using Pointer = SmartPointer< Self >
 
using Self = AdvancedTransform
 
using SpatialHessianType = FixedArray< Matrix< ScalarType, InputSpaceDimension, InputSpaceDimension >, OutputSpaceDimension >
 
using SpatialJacobianType = Matrix< ScalarType, OutputSpaceDimension, InputSpaceDimension >
 
using Superclass = Transform< TScalarType, NInputDimensions, NOutputDimensions >
 
using TransformType = Transform< TScalarType, NInputDimensions, NOutputDimensions >
 
using TransformTypeConstPointer = typename TransformType::ConstPointer
 
using TransformTypePointer = typename TransformType::Pointer
 

Public Member Functions

virtual const char * GetClassName () const
 
void GetJacobian (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const override
 
const ParametersType & GetParameters () const override
 
 ITK_DISALLOW_COPY_AND_MOVE (AffineDTI3DTransform)
 
 itkStaticConstMacro (InputSpaceDimension, unsigned int, 3)
 
 itkStaticConstMacro (OutputSpaceDimension, unsigned int, 3)
 
 itkStaticConstMacro (ParametersDimension, unsigned int, 12)
 
 itkStaticConstMacro (SpaceDimension, unsigned int, 3)
 
void SetIdentity () override
 
void SetParameters (const ParametersType &parameters) override
 
- Public Member Functions inherited from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >
const InputPointType & GetCenter () const
 
virtual const char * GetClassName () const
 
const FixedParametersType & GetFixedParameters () const override
 
void GetJacobian (const InputPointType &, JacobianType &, NonZeroJacobianIndicesType &) const override
 
void GetJacobianOfSpatialHessian (const InputPointType &, JacobianOfSpatialHessianType &, NonZeroJacobianIndicesType &) const override
 
void GetJacobianOfSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const override
 
void GetJacobianOfSpatialJacobian (const InputPointType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const override
 
void GetJacobianOfSpatialJacobian (const InputPointType &, SpatialJacobianType &, JacobianOfSpatialJacobianType &, NonZeroJacobianIndicesType &) const override
 
const MatrixTypeGetMatrix () const
 
const ParametersType & GetParameters () const override
 
void GetSpatialHessian (const InputPointType &, SpatialHessianType &) const override
 
void GetSpatialJacobian (const InputPointType &, SpatialJacobianType &) const override
 
TransformCategoryEnum GetTransformCategory () const override
 
const OutputVectorType & GetTranslation () const
 
bool IsLinear () const override
 
 itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)
 
 itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)
 
 itkStaticConstMacro (ParametersDimension, unsigned int, NOutputDimensions *(NInputDimensions+1))
 
void SetCenter (const InputPointType &center)
 
void SetFixedParameters (const FixedParametersType &) override
 
virtual void SetIdentity ()
 
virtual void SetMatrix (const MatrixType &matrix)
 
void SetParameters (const ParametersType &parameters) override
 
void SetTranslation (const OutputVectorType &translation)
 
OutputCovariantVectorType TransformCovariantVector (const InputCovariantVectorType &vector) const override
 
OutputPointType TransformPoint (const InputPointType &point) const override
 
OutputVectorType TransformVector (const InputVectorType &vector) const override
 
OutputVnlVectorType TransformVector (const InputVnlVectorType &vector) const override
 
- Public Member Functions inherited from itk::AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
void ComputeJacobianWithRespectToParameters (const InputPointType &, JacobianType &) const override
 
virtual void EvaluateJacobianWithImageGradientProduct (const InputPointType &inputPoint, const MovingImageGradientType &movingImageGradient, DerivativeType &imageJacobian, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const
 
virtual const char * GetClassName () const
 
virtual bool GetHasNonZeroJacobianOfSpatialHessian () const
 
virtual bool GetHasNonZeroSpatialHessian () const
 
virtual void GetJacobian (const InputPointType &inputPoint, JacobianType &j, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
 
virtual void GetJacobianOfSpatialHessian (const InputPointType &inputPoint, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
 
virtual void GetJacobianOfSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh, JacobianOfSpatialHessianType &jsh, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
 
virtual void GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
 
virtual void GetJacobianOfSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj, JacobianOfSpatialJacobianType &jsj, NonZeroJacobianIndicesType &nonZeroJacobianIndices) const =0
 
virtual NumberOfParametersType GetNumberOfNonZeroJacobianIndices () const
 
virtual void GetSpatialHessian (const InputPointType &inputPoint, SpatialHessianType &sh) const =0
 
virtual void GetSpatialJacobian (const InputPointType &inputPoint, SpatialJacobianType &sj) const =0
 
 ITK_DISALLOW_COPY_AND_MOVE (AdvancedTransform)
 
 itkStaticConstMacro (InputSpaceDimension, unsigned int, NInputDimensions)
 
 itkStaticConstMacro (OutputSpaceDimension, unsigned int, NOutputDimensions)
 

Static Public Member Functions

static Pointer New ()
 
- Static Public Member Functions inherited from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >
static Pointer New ()
 

Protected Member Functions

 AffineDTI3DTransform ()
 
 AffineDTI3DTransform (const MatrixType &matrix, const OutputPointType &offset)
 
 AffineDTI3DTransform (unsigned int outputSpaceDims, unsigned int paramsSpaceDims)
 
void ComputeMatrix () override
 
void ComputeMatrixParameters () override
 
virtual void PrecomputeJacobianOfSpatialJacobian ()
 
void PrintSelf (std::ostream &os, Indent indent) const override
 
void SetVarAngleScaleShear (ScalarArrayType angle, ScalarArrayType shear, ScalarArrayType scale)
 
 ~AffineDTI3DTransform () override=default
 
- Protected Member Functions inherited from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >
 AdvancedMatrixOffsetTransformBase (const unsigned int paramDims=ParametersDimension)
 
virtual void ComputeMatrix ()
 
virtual void ComputeMatrixParameters ()
 
virtual void ComputeOffset ()
 
void ComputeTranslation ()
 
const OutputVectorType & GetOffset () const
 
void PrintSelf (std::ostream &s, Indent indent) const override
 
void SetVarMatrix (const MatrixType &matrix)
 
void SetVarTranslation (const OutputVectorType &translation)
 
 ~AdvancedMatrixOffsetTransformBase () override=default
 
- Protected Member Functions inherited from itk::AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
 AdvancedTransform ()=default
 
 ~AdvancedTransform () override=default
 

Private Attributes

ScalarArrayType m_Angle
 
ScalarArrayType m_Scale
 
ScalarArrayType m_Shear
 

Additional Inherited Members

- Protected Attributes inherited from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >
JacobianOfSpatialHessianType m_JacobianOfSpatialHessian
 
JacobianOfSpatialJacobianType m_JacobianOfSpatialJacobian
 
NonZeroJacobianIndicesType m_NonZeroJacobianIndices
 
SpatialHessianType m_SpatialHessian
 
- Protected Attributes inherited from itk::AdvancedTransform< TScalarType, NInputDimensions, NOutputDimensions >
bool m_HasNonZeroJacobianOfSpatialHessian { true }
 
bool m_HasNonZeroSpatialHessian { true }
 

Member Typedef Documentation

◆ AngleType

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::AngleType = typename Superclass::ScalarType

Definition at line 118 of file itkAffineDTI3DTransform.h.

◆ CenterType

template<class TScalarType = double>
using itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >::CenterType = InputPointType

Typedefs.

Definition at line 147 of file itkAdvancedMatrixOffsetTransformBase.h.

◆ ConstPointer

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::ConstPointer = SmartPointer<const Self>

Definition at line 87 of file itkAffineDTI3DTransform.h.

◆ InverseMatrixType

template<class TScalarType = double>
using itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >::InverseMatrixType = Matrix<TScalarType, Self::InputSpaceDimension, Self::OutputSpaceDimension>

Standard inverse matrix type for this class.

Definition at line 144 of file itkAdvancedMatrixOffsetTransformBase.h.

◆ MatrixType

template<class TScalarType = double>
using itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >::MatrixType = Matrix<TScalarType, Self::OutputSpaceDimension, Self::InputSpaceDimension>

Standard matrix type for this class.

Definition at line 141 of file itkAdvancedMatrixOffsetTransformBase.h.

◆ OffsetType

template<class TScalarType = double>
using itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >::OffsetType = OutputVectorType

Definition at line 148 of file itkAdvancedMatrixOffsetTransformBase.h.

◆ Pointer

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::Pointer = SmartPointer<Self>

Definition at line 86 of file itkAffineDTI3DTransform.h.

◆ ScalarArrayType

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::ScalarArrayType = FixedArray<ScalarType>

Definition at line 127 of file itkAffineDTI3DTransform.h.

◆ Self

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::Self = AffineDTI3DTransform

Standard class typedefs.

Definition at line 84 of file itkAffineDTI3DTransform.h.

◆ Superclass

template<class TScalarType = double>
using itk::AffineDTI3DTransform< TScalarType >::Superclass = AdvancedMatrixOffsetTransformBase<TScalarType, 3, 3>

Definition at line 85 of file itkAffineDTI3DTransform.h.

◆ TranslationType

template<class TScalarType = double>
using itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >::TranslationType = OutputVectorType

Definition at line 149 of file itkAdvancedMatrixOffsetTransformBase.h.

Constructor & Destructor Documentation

◆ AffineDTI3DTransform() [1/3]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::AffineDTI3DTransform ( )
protected

◆ AffineDTI3DTransform() [2/3]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::AffineDTI3DTransform ( const MatrixType matrix,
const OutputPointType &  offset 
)
protected

◆ AffineDTI3DTransform() [3/3]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::AffineDTI3DTransform ( unsigned int  outputSpaceDims,
unsigned int  paramsSpaceDims 
)
protected

◆ ~AffineDTI3DTransform()

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::~AffineDTI3DTransform ( )
overrideprotecteddefault

Member Function Documentation

◆ ComputeMatrix()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::ComputeMatrix ( )
overrideprotectedvirtual

Compute the components of the rotation matrix in the superclass.

Reimplemented from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >.

◆ ComputeMatrixParameters()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::ComputeMatrixParameters ( )
overrideprotectedvirtual

◆ GetClassName()

template<class TScalarType = double>
virtual const char * itk::AffineDTI3DTransform< TScalarType >::GetClassName ( ) const
virtual

Run-time type information (and related methods).

Reimplemented from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >.

◆ GetJacobian()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::GetJacobian ( const InputPointType &  ,
JacobianType &  ,
NonZeroJacobianIndicesType  
) const
overridevirtual

Compute the Jacobian of the transformation.

Reimplemented from itk::AdvancedMatrixOffsetTransformBase< TScalarType, NInputDimensions, NOutputDimensions >.

◆ GetParameters()

template<class TScalarType = double>
const ParametersType & itk::AffineDTI3DTransform< TScalarType >::GetParameters ( ) const
override

◆ ITK_DISALLOW_COPY_AND_MOVE()

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::ITK_DISALLOW_COPY_AND_MOVE ( AffineDTI3DTransform< TScalarType )

◆ itkStaticConstMacro() [1/4]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::itkStaticConstMacro ( InputSpaceDimension  ,
unsigned int  ,
 
)

◆ itkStaticConstMacro() [2/4]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::itkStaticConstMacro ( OutputSpaceDimension  ,
unsigned int  ,
 
)

◆ itkStaticConstMacro() [3/4]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::itkStaticConstMacro ( ParametersDimension  ,
unsigned int  ,
12   
)

◆ itkStaticConstMacro() [4/4]

template<class TScalarType = double>
itk::AffineDTI3DTransform< TScalarType >::itkStaticConstMacro ( SpaceDimension  ,
unsigned int  ,
 
)

Dimension of the space.

◆ New()

template<class TScalarType = double>
static Pointer itk::AffineDTI3DTransform< TScalarType >::New ( )
static

New macro for creation of through a Smart Pointer.

◆ PrecomputeJacobianOfSpatialJacobian()

template<class TScalarType = double>
virtual void itk::AffineDTI3DTransform< TScalarType >::PrecomputeJacobianOfSpatialJacobian ( )
protectedvirtual

Update the m_JacobianOfSpatialJacobian.

◆ PrintSelf()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::PrintSelf ( std::ostream &  os,
Indent  indent 
) const
overrideprotected

◆ SetIdentity()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::SetIdentity ( )
overridevirtual

◆ SetParameters()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::SetParameters ( const ParametersType &  parameters)
override

Set/Get the transformation from a container of parameters This is typically used by optimizers. There are 12 parameters. [ Rx Ry Rz Gx Gy Gz Sx Sy Sz Tx Ty Tz ] ~rotation, scale, skew, translation

◆ SetVarAngleScaleShear()

template<class TScalarType = double>
void itk::AffineDTI3DTransform< TScalarType >::SetVarAngleScaleShear ( ScalarArrayType  angle,
ScalarArrayType  shear,
ScalarArrayType  scale 
)
protected

Set values of angles etc directly without recomputing other parameters.

Field Documentation

◆ m_Angle

template<class TScalarType = double>
ScalarArrayType itk::AffineDTI3DTransform< TScalarType >::m_Angle
private

Definition at line 173 of file itkAffineDTI3DTransform.h.

◆ m_Scale

template<class TScalarType = double>
ScalarArrayType itk::AffineDTI3DTransform< TScalarType >::m_Scale
private

Definition at line 175 of file itkAffineDTI3DTransform.h.

◆ m_Shear

template<class TScalarType = double>
ScalarArrayType itk::AffineDTI3DTransform< TScalarType >::m_Shear
private

Definition at line 174 of file itkAffineDTI3DTransform.h.



Generated on 2023-01-13 for elastix by doxygen 1.9.6 elastix logo